4lyk: Difference between revisions

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 ==Crystal structure of the EAL domain of c-di-GMP specific phosphodiesterase YahA in complex with activating cofactor Mg++==
-<StructureSection load='4lyk' size='340' side='right' caption='[[4lyk]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
+<StructureSection load='4lyk' size='340' side='right'caption='[[4lyk]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4lyk]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LYK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4LYK FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4lyk]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LYK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4LYK FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=HB0:TRANS-4-(HYDROXYMETHYL)CYCLOHEXANOL'>HB0</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=HB0:TRANS-4-(HYDROXYMETHYL)CYCLOHEXANOL'>HB0</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4kie|4kie]], [[4lj3|4lj3]]</td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4lyk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4lyk OCA], [https://pdbe.org/4lyk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4lyk RCSB], [https://www.ebi.ac.uk/pdbsum/4lyk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4lyk ProSAT]</span></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">b0315, JW0307, yahA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4lyk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4lyk OCA], [http://pdbe.org/4lyk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4lyk RCSB], [http://www.ebi.ac.uk/pdbsum/4lyk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4lyk ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/YAHA_ECOLI YAHA_ECOLI]] Hydrolyzes c-di-GMP (cyclic bis(3'-5') dimeric GMP) to 5'-pGpG, known as PDE-A activity. PDE-B activity, that is hydrolysis of 5'-pGpG to GMP, proceeds only very slowly.
+[https://www.uniprot.org/uniprot/PDEL_ECOLI PDEL_ECOLI] Acts both as an enzyme and as a c-di-GMP sensor to couple transcriptional activity to the c-di-GMP status of the cell (PubMed:26553851). Phosphodiesterase (PDE) that catalyzes the hydrolysis of cyclic-di-GMP (c-di-GMP) to 5'-pGpG (PubMed:15995192, PubMed:24451384, PubMed:26553851). Also acts as a transcription factor to control its own expression (PubMed:26553851).<ref>PMID:15995192</ref> <ref>PMID:24451384</ref> <ref>PMID:26553851</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 22: / Line 20: @@
 ==See Also==
-*[[Phosphodiesterase|Phosphodiesterase]]
+*[[Phosphodiesterase 3D structures|Phosphodiesterase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Ecoli]]
+[[Category: Escherichia coli K-12]]
-[[Category: Schirmer, T]]
+[[Category: Large Structures]]
-[[Category: Sundriyal, A]]
+[[Category: Schirmer T]]
-[[Category: Hydrolase]]
+[[Category: Sundriyal A]]
-[[Category: Pgpg]]
-[[Category: Phosphodiesterase]]
-[[Category: Tim-barrel]]